Various analytical instruments can be used for analyzing biological samples to identify peptides, proteins, and other biomolecules that are present in the sample. Mass spectrometry has gained prominence because of its ability to handle a wide variety of biomolecules with high sensitivity and rapid throughput. For example, proteins can be identified via analysis of spectra acquired using a tandem mass spectrometer. In some instances, the proteins are initially digested using a proteolytic agent to produce a variety of peptides, and the peptides are then analyzed by the tandem mass spectrometer to acquire a series of spectra.
In some instances, a tandem mass spectrometer is coupled to a chromatography system to analyze biomolecules present in a sample stream. For example, successive eluting portions of the sample stream can flow from a chromatography column, such as a High Performance Liquid Chromatography (“HPLC”) column, into the tandem mass spectrometer, and a series of spectra can be acquired from the eluting portions. While coupling of the tandem mass spectrometer to the chromatography system is desirable for a variety of reasons, such a configuration presents challenges in terms of efficiency at which mass spectrometry data can be acquired during a particular chromatography run. For example, based on analyzing a spectrum acquired from a particular eluting portion of a sample stream, it can be desirable to acquire additional spectra from that same eluting portion. However, the rate of elution of biomolecules present in the sample stream can be too fast for effective manual control of the tandem mass spectrometer. Also, it can be undesirable or impractical to interrupt a flow of the sample stream. In addition, there might be insufficient material for repeated analysis.
Current protocols in tandem mass spectrometry perform a single MS of a sample, and select, among all species observed, a subset of precursor ions for analysis by MS/MS. Both the precursor ions selected for MS/MS, and the parameters used during MS/MS, are selected to maximize the chances of being able to identify the primary sequence—the structure—of the precursor ion. In other words, decisions are made to obtain the highest number of good quality—identifiable—MS/MS spectra. A disadvantage of such an approach is that it does not try to directly increase the protein coverage or sensitivity of the acquisition. For example, an abundant protein whose peptides ionize well, should generate several precursor ions displaying high intensities by MS, and will consume instrument time that could be devoted to inspecting ions of lower intensity that belong to different proteins in the sample.
Consequently, in view of these shortcomings, in some settings a different discovery approach would be desirable.
What is needed, therefore, is a system and method of analyzing biological or chemical samples that can provide improved coverage and sensitivity for detecting specific proteins of interest.